You can use few options to update already deployed software.
1) Deploy the updater .pkg. If a .pkg updater does exist you can deploy this one which will be executed automatically on your FileWave Clients. Before going to use this option please make sure that the verification of all files in your fileset are set to 'Ignore at Verify'.
2) Build a new fileset that contains the update. Use FW XMagic to make a first snapshot of the testmachine you're going to deploy the fileset (to be updated) on it. On your test machine update the deployed software and make a second snapshot with FW XMagic. Create a new fileset and deploy it to your client machines. Before deploying this fileset make the original- already deployed fileset inactive.
An alternative execution is to set the old fileset to 'Ignore at Verify' and deploy the new one on top. After the Filesets Report indicates that the new fileset is active on all machines, you may delete the old fileset.
3) Build a fileset that contains only updated files. Deploy the fileset to a test machine. Then, use FW XMagic to take a snapshot of that machine. Update the deployed software and make a second snapshot with FW XMagic. Now you will get a list reporting all newly created and modified files. Mark only the new- and modified files to create a 'update' fileset of them. Now deploy this fileset to your client machines (test first! this method does not always work). Before deploying the update fileset, please make sure that the verification of the files in your old fileset are set to 'Ignore at Verify.'
4) Implement the updates in your original fileset. Complete option 3 and move all files from the update fileset into your original fileset. Replace files if they are already exist in your original fileset. Using this option you can leave the files verification on 'self healing'. For more instructions on this method, see the [url=http://http://www.filewave.org/viewtopic.php?t=635]Adobe CS2 Updating Instructions[/url]
To still ensure the full controll of all deployed files I would recommend to either use option 2, 3 or 4.